The Collapse of the Theory of Evolution in 20 Questions


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Horizontal gene transfer is essentially sideways heredity. It can even go from one kingdom of life into another, sideways, across great barriers. That was thought to be undoable. In fact, genes can go sideways across vast species boundaries. For instance, a gene for resistance to one kind of antibiotic in one form of bacteria, like staphylococcus, can move sideways into another, completely different form of bacteria, say, E.

This can happen not just in bacteria but also in animals, plants, and higher organisms, generally as a result of infection or parasitism.

One example is a form of transposon. Big, complicated word. But scientists have discovered that these things can also jump from one creature to another, and even from one species to another. Artist Emma Allen imagines the future of human evolution using face paint, a mirror, and a camera. Watch the progression from single-celled organism to cyborg unfold in this stunning animated self-portrait.

One transposon has been given the name space invaders. It seems able to pass, for instance, from a reptile into an insect or from a possum into a rat, by way of something called a kissing bug, an insect that, when sucking blood, sucks in some of this transposon. The transposon then moves from one species to another and becomes part of the heritable genome of that new species.

Explain the issues and how the latest science is rewriting the idea of natural selection. There are two phases in classic Darwinian evolution. First, there is the arising of variations from one creature to another or one individual population to another. That was thought to occur incrementally, in very slow stages, by mutations in the genome. Once there are variations among individuals, natural selection, the survival of the fittest, acts upon those variations. But horizontal gene transfer has revealed that nature does sometimes make leaps, whereby huge lumps of DNA can appear in an individual or population quite suddenly and then natural selection acts on them.

That can be a very important mechanism in the evolution of new species.

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Intelligent design

Most of us are unaware of just how many bacteria are swarming in our gut or armpits. Take us inside our microbiome and explain how it is crucial for human health. We now realize, because we can sequence genomes, that we have great populations of bacteria living within us. In fact, there are hundreds, if not thousands, of different kinds of bacteria that live benignly within our guts, armpits, ears, noses, pores, or on our skin. This is known as the human microbiome. The maintenance of that ecosystem of microbes is essential to human health, which is one reason why the over-use of antibiotics can be a bad thing.

Most antibiotics tend to be broad range. We now understand that we humans, along with most other creatures, are composites of other creatures. Not just the microbiome living in our bellies and intestines, but creatures that have over time become inserted in our very cells.

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Every cell in the human body contains, for instance, little mechanisms that help package energy. Those are called mitochondria. We now realize that those mitochondria are the descendants of captured bacteria that were either swallowed by, or infected, the cells that became complex cells of all animals and plants. Likewise, 8 percent of the human genome, we now know, is viral DNA, which has come into our lineage by infection over the last million years or so.

Some of that viral DNA is still functioning as genes that are important for human life and reproduction. Tell us about it and how it is revolutionizing biology and genetics. CRISPR is an acronym for a gene-editing tool discovered in the last years that is very powerful and inexpensive. Each film, each fingerprint, represented ribosomal RNA from a different creature. The work was deceptively perilous. Sogin described to me the deliveries of radioactive phosphorus an isotope designated as P 32 , with a half-life of 14 days , which amounted to a sizable quantity arriving every other Monday.

Sogin would draw out a measured amount of the liquid and add it to whatever bacterial culture he intended to process next. By , the Woese lab had become one of the foremost users of such RNA-sequencing technology in the world. While the grad students and technicians produced fingerprints, Woese spent his time staring at the spots. Was this effort tedious in practice as well as profound in its potential results? Failing initially to persuade Woese of his aptitude for that, Fox was banished back to the lab, set to the tasks of growing radioactive cells and extracting their ribosomal RNA.


  1. B. Zavadovsky: The "Physical" and "Biological" in the Process of Organic Evolution.
  2. 11.5: Common Misconceptions about Evolution.
  3. Stephen Jay Gould - Wikipedia.

But he continued, in flashes, to show his value to Woese as a thinker. That offended some scientists. Another factor was that Woese lacked facility as an explainer. He had never developed the skills to give a good lecture. Rockets took off, and they wrote the most unscientific nonsense you can imagine. Wolfe himself heard from colleagues immediately.


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  • Among his phone calls on the morning of Nov. He never called back. But the broader damage was done. The scientific community just totally rejected the thing. As a result, this whole concept was set back by at least a decade or 15 years. In Woese received a MacArthur Fellowship for his efforts in phylogenetic analysis and his discovery of the archaea, and in he was elected to the National Academy of Sciences. Despite the MacArthur honor, and because the Academy had elected him relatively late at 59 , he still thought of himself as a neglected outsider.

    That gave him some latitude to continue being ambitious, bold and ornery. And he wanted to revisit the status of his beloved archaea. As an outlet for this work, Woese turned to the Proceedings of the National Academy of Sciences, a journal in which — as a member now of the Academy — he could be a bit more speculative than he would at Nature or Science.

    Second, there should be three major divisions of life, not two the predominant view , not five an alternative proposal, recognizing animals, plants, bacteria, fungi and a catchall group of other eukaryotes , and those divisions should be known as domains. Three domains, recognized above the old kingdoms rather than replacing them: It was ingenious strategically, transcending rather than rejoining the battle over kingdoms. And of course there was a tree. It was drawn in straight, simple lines, but it was rich and provocative nonetheless.

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    It was the last of the great classical trees, authoritative, profound, completely new to science and correct to some degree. But it only served as a point of departure for what came next. The following decade saw an explosive recognition of the bizarre, counterintuitive phenomenon called horizontal gene transfer and the role it has played throughout the history of life.

    The first recognition by science that any such thing as H. To say that seemed odd is an understatement. Still more unexpectedly, as later work would reveal, H. Slowly at first, during the s and early s, H. But then, as new tools and methods made gene sequencing easier and faster, and as more powerful computers allowed analysis of the vast troves of genomic data, researchers went far beyond 16S rRNA, comparing other genes and whole genomes.


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    • What they found surprised them: that many genes had moved sideways from one lineage of life into another. Such genes might be absent from most living species within a group say, a family of butterfly species , implying that it was absent too from the common ancestral form, but it might show up unexpectedly in one species of butterfly in that family, matching closely to a gene that exists only in another kind of creature say, a bacterium , classified to an entirely different part of the tree of life.

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      How could that happen? Researchers have identified three primary mechanisms by which H. Transformation is what Fred Griffith noticed in uptake of naked DNA, left floating in the environment after the rupture of some living cell, by another living cell again, not necessarily of the same species. Transduction is a sort of drag-and-drop trick performed by viruses, picking up bits of DNA from cells they infect, then dropping those DNA bits later within other infected cells, where they may become incorporated into the genomes.

      Conjugation was known to be widespread and common among bacteria. Then improved genome sequencing and closer scrutiny brought more surprises. A bacterium had sent bits of its DNA into the nuclear genomes of infected plants. How was that possible? A species of sea urchin seemed to have shared one of its genes with a very different species of sea urchin, from which its lineage diverged millions of years earlier.

      That was a stretch. Still another bacterium, the familiar E. New investigations, as time passed and improvements in gene-sequencing technology made more complete genomes available, showed that far more radical leaps were happening, and not infrequently. Rotifers are homely beyond imagining. They live in water, mainly freshwater, and in moist environments such as soils and mosses, rain gutters and sewage-treatment tanks.

      Some species favor harsh, changeable environments that sometimes go dry, and their individuals reproduce without sex. Despite the absence of sexual recombination, which shuffles the genetic deck in a population and offers new combinations of genes, these rotifers have managed to find newness by other means. One means is horizontal gene transfer.

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      More specifically, they found at least 22 genes from other creatures, most of which, they concluded, must have arrived by H. Some of those were bacterial genes, some were fungal. One gene had come from a plant. At least a few of those genes were still functional, producing enzymes or other products useful to the rotifer. Some of these individual cases were later challenged, but the trend of discoveries held. Again this was supposed to be impossible.

      There were fervent doubters. Alien genes cannot move from one species to another, they insisted. The germ line of animals, meaning the eggs and the sperm and the reproductive cells that give rise to them, is held separate from such influences. Bacteria cannot cross that barricade, the Weismann barrier — so said the skeptical view — to insert bits of their own DNA into animal genomes. But again it turned out to be possible. Beyond the realm of insects and rotifers, evidence of H. Even the human genome has been laterally invaded. Its sequencing has revealed the boggling reality that 8 percent of our human genome consists of viral DNA inserted sideways into our lineage by retroviruses.

      Some of those viral genes, as illuminated by a French scientist named Thierry Heidmann and his colleagues, have even been co-opted to function in human physiology, such as creating an essential layer between the placenta and the fetus during pregnancy. These and other discoveries of H. Carl Woese, as his research career ended, assumed his new role as a much-honored but cranky elder, with strong opinions.

      He collected kudos, and he wrote. The Crafoord was gratifying, but he seems to have yearned for more. Woese had a sort of bifurcated brain, one of his oldest friends, Larry Gold, told me. Gold, now a distinguished molecular biologist and biotech entrepreneur, knew Woese from the early days in Schenectady when they both worked for G. On one side of Woese, he said, was this great depth of learning — mostly acquired by self-instruction, not formal training — and a relentless questioning. Woese had trained at Yale as a biophysicist, Gold reminded me, not a biologist.

      He was thinking about what happened 3. But the deep history, going back those billions of years, lay at the core of understanding evolution, as Woese tried to do it. One year after the Crafoord Prize, in , he published another of his big, ambitious treatises. This appeared not in Nature or Science but in a narrower journal, Microbiology and Molecular Biology Reviews, the editors of which allowed him 14 pages to vent.

      It was an appropriate outlet, not just a spacious one, because he wanted to tell the field of molecular biology just what he thought of it. He wanted to piss in the punch bowl. It lost interest, or never had any, in the big story over four billion years. What a stunning example of a biology that operates from an engineering perspective, a biology that has no genuine guiding vision! No one ever accused Woese of pulling his punches.

      And as he got older, ever more pugnacious, he harbored an increasing disdain for Charles Darwin, distinct from but alongside his disdain for molecular biology. The Darwin animus had kindled within him, an off-and-on resentment of the distant figure with the big name. Part of it might have been substantive disagreement: Darwin himself, and the neo-Darwinian synthesis of ideas that became orthodoxy during the 20th century, saw evolutionary change as inherently incremental and gave little attention to the processes of inheritance, variation and reproduction as they occur among microbes, as opposed to animals and plants.

      Woese saw microbial evolution and later in his life H. Another part was probably sheer jealousy. He came to believe himself a more important, more profound and more revolutionary thinker than Darwin himself. Woese was bitter and needy toward the end of his life. Among the essential points of the upheaval that Woese helped initiate are three counterintuitive insights, three challenges to categorical thinking about aspects of life on earth.

      The categoricals are these: species, individual, tree. Individual: An organism is also discrete, with a unitary identity. No mixing refutes the oneness of an individual. Tree: Inheritance flows always vertically from ancestor to descendant, always branching and diverging, never converging. So the history of life is shaped like a tree. Now we know, thanks to Carl Woese and those who have followed him, that each of those three categoricals is wrong. It was pancreatic cancer. He sent for his trusted administrative assistant and friend, Debbie Piper, to join him and his family.

      She flew into Boston, and he pleaded with her to rescue him from Massachusetts General Hospital and the mind-dulling medication he was given after surgery. He wanted clarity more than he wanted comfort. That August, he consented to endure a series of video interviews for the historical record. Several friends came to town for that purpose, to assist in the questioning, and Woese did his best to respond, with halting reflections on his work, his discoveries, the science of his time. Pale and manifestly uncomfortable, seated before bookshelves and an ivy plant, he spoke to the camera for seven hours spread across three days, laboring to remember facts and names, to express ideas, frustrated when he was unable to.

      There was so much that still needed saying. Now it was too late.

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      He took long pauses. He blinked back his own mortality. At the time of his memorial service, months afterward, someone raised the idea of playing some of this video to bring his voice and image into the event. Because he just looks and sounds like a sick old man. But inside the sick old man was a multiplicity of other realities. Some had arisen straight, and some had arrived sideways. Sign up for our newsletter to get the best of The New York Times Magazine delivered to your inbox every week.

      Supported by. Lyons, began: Scientists studying the evolution of primitive organisms reported today the existence of a separate form of life that is hard to find in nature.

      The Collapse of the Theory of Evolution in 20 Questions The Collapse of the Theory of Evolution in 20 Questions
      The Collapse of the Theory of Evolution in 20 Questions The Collapse of the Theory of Evolution in 20 Questions
      The Collapse of the Theory of Evolution in 20 Questions The Collapse of the Theory of Evolution in 20 Questions
      The Collapse of the Theory of Evolution in 20 Questions The Collapse of the Theory of Evolution in 20 Questions
      The Collapse of the Theory of Evolution in 20 Questions The Collapse of the Theory of Evolution in 20 Questions
      The Collapse of the Theory of Evolution in 20 Questions The Collapse of the Theory of Evolution in 20 Questions
      The Collapse of the Theory of Evolution in 20 Questions The Collapse of the Theory of Evolution in 20 Questions
      The Collapse of the Theory of Evolution in 20 Questions The Collapse of the Theory of Evolution in 20 Questions

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